Contacts of the strand formed by residues 6 - 15 (chain A) in PDB entry 2CT8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.2 44.2 + - - +
2A THR* 3.5 19.1 - - - +
4A MET 3.9 2.2 - - - +
5A LYS* 1.3 76.7 - - - +
7A PHE* 1.3 68.0 + - - +
8A TYR* 4.2 1.4 - - - +
43A TYR* 4.1 9.4 - - - -
44A ASP* 3.1 24.7 - - + +
247A ILE* 3.5 14.8 - - + +
248A TYR* 3.2 25.0 + - + +
250A PRO 2.7 29.9 + - - -
252A ASP* 2.9 23.9 + - - +
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Residues in contact with PHE 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 1.3 77.8 - - - +
8A TYR* 1.3 59.6 + - - +
9A VAL* 3.8 23.6 - - + -
34A ILE* 4.0 21.8 - - + -
35A ALA* 4.9 0.7 - - - -
38A TYR* 3.4 63.3 - + + -
43A TYR* 4.4 5.3 - + + -
44A ASP 3.1 5.9 + - - +
45A VAL* 3.2 15.7 - - + +
46A PHE* 2.9 24.1 + - - +
248A TYR* 5.1 0.4 - - - -
252A ASP* 3.3 32.3 - - + -
253A LEU* 3.8 25.8 - - + -
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Residues in contact with TYR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 4.2 2.9 - - + +
7A PHE* 1.3 74.8 - - - +
9A VAL* 1.3 67.0 + - - +
10A THR* 3.3 28.8 - - + +
46A PHE* 3.3 36.1 - + + -
48A LEU* 3.4 15.6 - - + +
237A TYR 2.7 28.7 + - - -
241A LEU* 3.7 20.9 - - + +
248A TYR* 3.4 24.7 - - + +
249A TRP* 3.3 30.3 - + - -
251A ALA* 3.7 12.7 - - + +
252A ASP* 2.9 34.7 + - - +
253A LEU 3.2 7.7 + - - +
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.8 18.6 - - + -
8A TYR* 1.3 74.5 - - - +
10A THR* 1.3 76.0 + - - +
31A ALA* 4.4 4.3 - - + +
34A ILE* 4.0 27.4 - - + -
35A ALA* 4.3 7.2 - - + -
45A VAL* 4.9 0.4 - - + -
46A PHE 2.9 16.2 + - - +
47A PHE* 4.0 21.5 - - + -
48A LEU 2.9 23.9 + - - -
253A LEU* 3.2 21.1 - - + +
255A LEU* 4.2 12.1 - - + -
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Residues in contact with THR 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 3.3 36.3 - - + +
9A VAL* 1.3 85.1 - - - +
11A THR* 1.3 63.1 + - - +
48A LEU* 3.5 13.5 - - + -
237A TYR* 3.4 26.0 - - + -
251A ALA* 5.1 0.7 - - + -
253A LEU 3.1 2.4 + - - +
254A HIS* 2.6 34.5 + - + +
255A LEU* 2.9 31.2 + - - +
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Residues in contact with THR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 1.3 75.1 - - - +
12A PRO* 1.3 81.4 + - - +
13A ILE* 5.0 1.2 - - - +
14A TYR* 3.6 7.9 + - - +
27A THR* 3.9 4.0 - - - +
28A THR* 3.9 17.3 - - - +
31A ALA* 3.4 31.6 - - + -
47A PHE* 3.7 14.1 - - + -
48A LEU* 3.2 5.3 + - - +
49A THR* 2.9 28.9 + - - -
237A TYR* 3.5 17.2 - - - -
255A LEU* 3.6 4.9 - - - -
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Residues in contact with PRO 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 1.3 103.5 + - - +
13A ILE* 1.3 61.9 + - - +
14A TYR* 3.5 25.0 + - + +
27A THR* 3.3 13.2 - - + -
49A THR* 4.2 0.9 + - - -
50A GLY 4.1 1.0 + - - +
237A TYR* 3.8 10.8 - - - +
255A LEU 3.2 16.8 - - - +
256A VAL* 3.9 11.2 - - + -
260A ILE* 4.8 2.2 - - + -
501A MSP 3.3 48.7 - - + +
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR 5.0 2.0 - - - +
12A PRO* 1.3 73.1 - - - +
14A TYR* 1.3 55.3 + - - +
49A THR* 4.6 1.1 - - - -
50A GLY* 3.3 32.1 - - - +
51A THR 3.8 4.5 - - - +
52A ASP* 3.4 6.6 - - + +
95A ILE* 4.3 6.1 - - + +
97A THR* 3.4 32.5 - - + -
233A ALA* 3.5 30.3 - - + +
236A ASN* 3.4 30.0 - - + +
501A MSP 2.7 51.9 + - + +
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Residues in contact with TYR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 3.6 6.7 - - - -
12A PRO* 3.6 22.2 - - + -
13A ILE* 1.3 72.7 - - - +
15A TYR* 1.3 62.5 + - - +
24A HIS* 3.0 22.0 + + + -
27A THR* 3.4 15.8 - - - -
28A THR* 2.6 30.3 + - - -
49A THR* 3.8 9.2 - - - -
50A GLY 3.0 13.9 + - - +
51A THR* 3.1 12.3 - - - +
52A ASP 2.8 22.2 + - - -
80A PHE* 3.6 36.8 - + + -
84A TRP* 3.5 14.4 - + - -
501A MSP 3.1 47.3 - - - +
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Residues in contact with TYR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 1.3 74.1 - - - +
16A VAL* 1.3 60.3 + - - +
17A ASN* 3.5 17.8 + - + +
18A ASP* 4.3 4.9 + - - +
24A HIS* 5.1 2.9 - - - -
52A ASP* 3.3 28.3 + - - -
54A HIS 5.5 4.5 - - - -
57A LYS* 4.0 22.9 - - - -
80A PHE* 3.4 17.7 - - - -
229A VAL* 5.4 9.3 - - + +
230A TRP* 3.5 27.0 + - - -
501A MSP 3.1 64.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il